Microbial assemblage dynamics within the American alligator nesting ecosystem: Metagenome Analysis

Understanding the ecological processes that shape species assemblage patterns is central to community ecology. The effects of ecological processes on assemblage patterns are scale dependent. Research that addresses community patterns at different focal scales may discern distinct process structuring conclusions. Here, we use metabarcoding and shotgun sequencing to determine bacterial taxonomic and functional assemblage patterns among varying focal scales (micro-, meso-, macro-) within the American alligator (Alligator mississippiensis) nesting microbiome. We correlate bacterial assemblage patterns amid eight defined compartments within and proximal to alligator nests (micro-), among 17 nests (meso-), and between three geographic sampling sites (macro-), to discern which ecological processes may drive bacterial assemblage patterns within the nesting environment. Among all focal scales, bacterial taxonomic and functional richness (a-diversity) did not statistically differ. In contrast, bacterial composition (ß-diversity) was unique across focal scales, with nests predicting the highest degree of assemblage variation. Functional pathways were redundant within nests but dissimilar between geographic locations. Considering these observed scale-based patterns, alligator nest bacterial taxonomic composition may be shaped by distinct environmental filters and/or dispersal limitations but are under somewhat redundant functional selection. These findings advance pattern-process dynamics within the field of microbial community ecology and describe processes influencing the American alligator nest microbiome.